Allogeneic stem cell transplantation (Allo-SCT) remains an option for patients with follicular lymphoma (FL). We performed a retrospective analysis to examine long-term disease control and treatment-related mortality (TRM) in a group of patients that underwent transplant for clinically high-risk disease. Thirty-seven patients with indolent FL (follicular small cleaved [FSC], follicular mixed [FM] or FL grades 1 or 2 by WHO criteria) underwent allo-SCT. Patients were in a chemosensitive remission at the time of SCT. The conditioning regimen was typically busulfan-cyclophosphamide (BuCy). Cyclophosphamide-total body irradiation (TBI) was used for unrelated donor SCT. The median age at the time of transplant was 45 years (range: 24-58). The median number of prior chemotherapy regimens was 3 (range: 1-6). Thirty-seven patients received BuCy conditioning and 2 patients underwent reduced intensity conditioning SCT. Seventy-two percent of patients had a matched sibling donor. With a median follow-up of 63.5 months in survivors, the 5-year overall survival is 79.1% (95% confidence interval 66.3%-94.4%). TRM was 15.4%, with an additional case of mortality from breast cancer. These results demonstrate that in selected younger patients, a fully myeloablative allo-SCT utilizing BuCy conditioning provides excellent OS and disease control with low TRM.